52 lines
1.7 KiB
Java
52 lines
1.7 KiB
Java
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/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2008 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.picard.variation;
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import java.io.File;
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import edu.mit.broad.picard.cmdline.CommandLineProgram;
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import edu.mit.broad.picard.cmdline.Option;
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import edu.mit.broad.picard.cmdline.Usage;
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/**
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* CommandLineProgram to generate to invoke DbSnpFileGenerator
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*
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* @author Kathleen Tibbetts
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*/
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public class GenerateDbSnpFile extends CommandLineProgram
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{
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// The following attributes define the command-line arguments
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@Usage(programVersion="1.0")
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public String USAGE =
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"Usage: " + getClass().getName() + " [options]\n\n" +
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"Generate a KnownVariant binary file from a UCSC DbSnp text file.\n";
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@Option(shortName = "S", doc = "UCSC SNP file. ")
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public File SNP_FILE;
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@Option(shortName = "D", doc = "Sequence Dictionary for the genome in SAM or BAM format. ")
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public File SEQUENCE_DICTIONARY;
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@Option(shortName = "O", doc = "The binary output file. ")
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public File OUTPUT;
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@Override
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protected int doWork() {
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DbSnpFileGenerator generator = new DbSnpFileGenerator(SNP_FILE, SEQUENCE_DICTIONARY, OUTPUT);
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generator.writeDbSnpFile();
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return 0;
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}
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public static void main(String[] argv) {
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System.exit(new GenerateDbSnpFile().instanceMain(argv));
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}
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}
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